Mercurial > repos > iarc > mutspec
changeset 4:916846f73e25 draft
Uploaded
| author | iarc |
|---|---|
| date | Fri, 29 Apr 2016 05:11:28 -0400 |
| parents | 14fe7238c6d7 |
| children | 097ae310ced0 |
| files | Frequency-COSMICv72-Hupki-Others.txt R/compareSignature_Galaxy.r hg18_listAVDB.txt hg19_listAVDB.txt hg38_listAVDB.txt mm10_listAVDB.txt mutspecAnnot.pl mutspecAnnot.xml mutspecCompare.xml mutspecFilter.pl mutspecFilter.xml mutspecNmf.xml mutspecNmf_wrapper.sh mutspecSplit.xml mutspecStat.xml mutspecStat_wrapper.sh rn6_listAVDB.txt tool_dependencies.xml |
| diffstat | 18 files changed, 304 insertions(+), 38 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Frequency-COSMICv72-Hupki-Others.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,97 @@ +Substitution Type Trinucleotide Somatic Mutation Type Signature 1 Signature 2 Signature 3 Signature 4 Signature 5 Signature 6 Signature 7 Signature 8 Signature 9 Signature 10 Signature 11 Signature 12 Signature 13 Signature 14 Signature 15 Signature 16 Signature 17 Signature 18 Signature 19 Signature 20 Signature 21 Signature 22 Signature 23 Signature 24 Signature 25 Signature 26 Signature 27 Signature 28 Signature 29 Signature 30 Signature 1 MEF Signature 2 MEF Signature 3 MEF Signature 5 MEF Signature DMBA Signature MNU Signature Urethane +C>A ACA A[C>A]A 0.0110983262 0.0006827082 0.0221723068 0.0365 0.0149415477 0.0017 0.0004 0.0367180038 0.012 0.0007 0.0002 0.0077 0.0003347572 0.0001 0.0013 0.0161 0.0018320192 0.0505364186 0.0107 0.0011799616 0.0001 0.0015040704 0.0004533607 0.0286459925 0.009896768 0.0020397729 0.0052056269 0.0013974388 0.0699819873 0 0.000781083 0.0037229109 0.0283533537 0.0003710632 0.0121138158 0.0010972115 0.0044388346 +C>A ACC A[C>A]C 0.0091493407 0.0006191072 0.0178716754 0.0309 0.008960918 0.0028 0.0005 0.0332457222 0.0067 0.001 0.001 0.0047 0.0006487361 0.0042 0.004 0.0097 0.0003422356 0.0109398248 0.0074 0.0022115051 0.0007 0.002451011 0.0003668005 0.0202146384 0.0069989288 0.0014871623 0.0047382274 0.0009171877 0.0551523572 0 0.0022972224 0.0070460466 0.015676074 0.001672691 0.0046539767 0.0009508214 0.0004001609 +C>A ACG A[C>A]G 0.0014900705 0.000099279 0.0021383396 0.0183 0.002207846 0.0005 0 0.0025253113 0.0005 0.0003 0 0.0017 3.8144594E-005 0.0005 0 0.0022 1.576225E-006 0.0022880727 0.0005 1.61691E-007 0 0 0 0.0204789965 0.001448443 0.0002839456 0.0007826979 0 0.017846984 0.0019673 0.0031701397 0.0025537924 0.0272331284 0.0007812591 0.0071227909 0.0003972991 1.63618104265282E-020 +C>A ACT A[C>A]T 0.0062338852 0.0003238914 0.0162651456 0.0243 0.0092069053 0.0019 0.0004 0.0335985495 0.0068 0.0092 0.0002 0.0046 0.0008466585 0.0296 0.0057 0.0088 0.0031796648 0.0194240914 0.0074 0.00300801 0.0006 0.0009224525 0 0.0246001454 0.004966565 0.0005978656 0.0027182425 0.00051341 0.026804716 0 0.0015620621 0.0104484061 0.0079498813 0.0004287024 0.0083172408 0.0002539234 0.0015287933 +C>A CCA C[C>A]A 0.0065958701 0.000677445 0.0187817256 0.0461 0.0096749043 0.0101 0.0012 0.0317237566 0.0098 0.0031 0.0007 0.0135 0.0017100896 0.0056 0.0106 0.0159 0.0010324302 0.0887681088 0.0112 0.0173771106 0.002 0.0045496929 0.0001647394 0.0635592838 0.0148329479 0.0037058501 0.0050650733 0.0011685156 0.0514102117 0 0.0094052338 0.0035222831 0.0414403498 0.0050521059 0.0224513894 0.0008540231 0.0031599431 +C>A CCC C[C>A]C 0.0073423678 0.000213681 0.0157604578 0.0614 0.0049523006 0.0241 0.0006 0.0255054071 0.0057 0.0009 0.0017 0.0112 0.0011592566 0.0102 0.0084 0.01 0.0004218801 0.0206413906 0.0159 0.036502463 0.0014 0.0037644739 0.0007368748 0.0337570047 0.0078221753 0.0039807234 0.0022341533 0.0003342918 0.0258256508 0 0.0031118726 0.0059886212 0.0390237536 0.0007556355 0.0096511373 0.0007989301 0.0042099735 +C>A CCG C[C>A]G 0.0008928404 6.77046E-006 0.0019633898 0.0088 0.0028006273 0.0091 0 0.0011596243 0 0.0007 0.001 0.0028 0.0002441665 0.0009 0.0015 0.0022 0.0002974628 0.0171784025 0.0018 0.0124825875 0.0027 0.0009001633 0.0001639537 0.0224289858 0.0012769767 0.000811742 0.0002663122 0.000053652 0.0144961833 0.0022624 0.0031056722 0.0027351313 0.0444175322 0.000426758 0.0104292165 0.0004936949 0.001053447 +C>A CCT C[C>A]T 0.0071865816 0.0004163329 0.0147228611 0.0432 0.0110134658 0.0571 0.0013 0.028791173 0.0091 0.016 0.0014 0.0071 0.0012567682 0.1257 0.0228 0.0084 3.1479429E-005 0.0376769589 0.0096 0.1034012262 0.0056 0.0044398462 0.0007227318 0.0200865154 0.0125636547 0.0190384313 0.00310057 0.0001866719 0.0403550741 0 0.0069708534 0.0135089174 0.0262144919 0.0012449334 0.0241632334 0.0004829446 0.0011918687 +C>A GCA G[C>A]A 0.008232604 0.0003520134 0.0096965397 0.0376 0.011892169 0.0024 0.0003 0.0236823289 0.0118 0.0014 0.0004 0.0062 0.0001321096 0.0018 0.0024 0.0096 0.0065354049 0.1287241581 0.0032 0.0011161238 0.0001 0.0012983702 0.0003499075 0.0546764487 0.0134652951 0.0013753118 0.0107558719 0.0021366291 0.0780466101 0.008853 0.0038823793 0.0123398664 0.0263977944 0.0008119624 0.0094122013 0.0006917252 0.004280167 +C>A GCC G[C>A]C 0.0057580214 0.0001338169 0.0108433411 0.0399 0.0092478575 0.0058 0.0001 0.0158218964 0.0092 0.0022 0.001 0.0056 0.000754244 0.0114 0.0099 0.0094 0.001293804 0.0160928787 0.0031 0.0032714286 0.0038 0.0018096222 0.0005683378 0.109945989 0.0064682981 0.0019616391 0.0124423351 0.0004292084 0.0734609147 0.0093449 0.0070583387 0.0107953358 0.031326093 0.002913003 0.0031021377 0.0010116809 0.003792303 +C>A GCG G[C>A]G 0.0006163352 0.0001784417 0.0009291405 0.0227 0.0028091885 0.0021 0 0.0008509138 0 0.0002 0 0.0015 9.6820775E-005 0.0011 0.0013 0.0036 0.0012836634 0.0092714168 0 0.0037516125 0.0003 0.0003338381 0.0001494178 0.046524869 0.0006581031 1.3229664E-005 0.0016296283 0 0.0173832969 0.0008853 0.0015395666 0.0021848297 0.0263967356 2.28346914246428E-020 0.0025774017 0.000128266 0.0017525461 +C>A GCT G[C>A]T 0.0044590803 0.000122832 0.0122153826 0.0258 0.0103012675 0.0087 0.0001 0.0210612358 0.0085 0.0088 0.0006 0.0027 0.0005511037 0.0736 0.0309 0.0063 0.0031037667 0.0720170701 0.0072 0.0129371945 0.0023 0.0005191482 0 0.0504287095 0.0104730803 0.0019349963 0.0074123552 0.0013185073 0.0596024721 0.0081645 0.0046277367 0.0141566067 0.0151523048 0.0012329031 0.0074480381 0.0009433454 0.0025903332 +C>A TCA T[C>A]A 0.0122500637 0.0151274275 0.0116532249 0.033 0.0147740162 0.0017 0.001 0.027032383 0.0222 0.0374 0.0009 0.0066 0.0481660479 0.0005 0.0057 0.0122 0.0018245583 0.0670806435 0.0051 0.0006882997 0.0001 0.0040516346 0.00207129 0.0314512632 0.0069381466 0.0026800624 0.0070792845 0.0007759028 0.0268944065 0 0.0087885822 0.0073157468 0.0118931991 0.0020899667 0.0100747618 1.06168434038267E-020 0.0011099646 +C>A TCC T[C>A]C 0.0111622293 0.0065324925 0.016606775 0.0538 0.012043465 0.0029 0.002 0.0180897733 0.0043 0.0103 0.0025 0.0099 0.0173295571 0.0166 0.0062 0.0145 0.0012865183 0.0418690097 0.0063 0.0040582291 0.0005 0.0027397709 0.0006964102 0.0625382937 0.0102466074 0.0020316439 0.0062688006 0.0008292925 0.031608137 0 0.0045906893 0.0055555952 0.0228092194 0.0029764847 0.0110724052 0.0011826955 0.0028809145 +C>A TCG T[C>A]G 0.0022754957 0.0016564554 0.0013572394 0.0104 0.0039023624 0.0011 0.0002 0.0016948752 0 0.0031 0.0001 0.0019 0.0022931573 0 0.0025 0.004 0.002172942 0.0151623793 0.0018 0.0010011022 0 0.0005131511 9.9393633E-005 0.0128025907 0 0.0002650717 0.0014464034 0 0.0125004682 0.0016722 0.0007774908 3.70860800590008E-020 0.0151191495 2.28346914246428E-020 0.0080051329 0.000084525 1.63618104265282E-020 +C>A TCT T[C>A]T 0.0152591025 0.0123946107 0.016328076 0.037 0.0182433957 0.0058 0.0013 0.0381413309 0.0322 0.3083 0.0004 0.0049 0.0186345815 0.0516 0.0145 0.0157 0.0050123164 0.1178778467 0.0087 0.0122291045 0.0004 0.0036056509 0.0002074302 0.0302976796 0.0246257872 0.0030171875 0.0098062778 0.0019980737 0.0412071764 0 0.0056468497 0.0041456849 0.016509629 0.0003531941 0.0142205963 0.0004051506 0.0027466457 +C>G ACA A[C>G]A 0.0018010684 0.000263481 0.0240026152 0.0097 0.0116710217 0.0013 0 0.0083568448 0.0048 0.0005 0.0007 0.0031 0.0037751653 0.0001 0.0011 0.0048 0.0016617042 0.0015168876 0.0058 0.0006970411 0.0005 0.000527644 0 0.0119930388 0.0080325676 0.0012728813 0.0013241632 0.000255195 0.0093019711 0 0.0039109532 0.0052086941 0.0112040012 0.0008072133 0.0032995837 0.0011280933 0.0051661719 +C>G ACC A[C>G]C 0.0025809085 0.000269866 0.0121603037 0.0054 0.0072920886 0.0012 0 0.0043063803 0.0023 0.0003 0.0003 0.0015 0.0009208248 0 0.0001 0.0024 0.0016268984 0.0024987845 0.0019 0.00205931 0.0008 0 0 0.0084251198 0.0016359704 0.0015281949 0.0017710841 0.000268899 0.0034790489 0 0.0038915791 0.0021914116 0.004675425 2.28346914246428E-020 0.0017490163 0.0001014437 1.63618104265282E-020 +C>G ACG A[C>G]G 0.000592548 0.0002192339 0.0052754195 0.0031 0.0023038392 0 0 0.0005844153 0 0 0 0 1.9890489E-005 0 0.0006 0 2.5801897E-005 0.002614509 0 0.000012735 0 0 0 0 0 0.0003072463 0 0 0.0001544335 0.00482 0.0015371874 3.70860800590008E-020 0.0113226789 2.28346914246428E-020 0.001844425 0.0001180292 0.0007772772 +C>G ACT A[C>G]T 0.0029639863 0.0006109735 0.0232776563 0.0054 0.0116962457 0.0018 0.0001 0.0086349069 0.0038 0.0002 0.0009 0.0025 0.0038606325 0.0001 0.001 0.0073 0.0013285076 0.0039830112 0.0072 0.0008485871 0.0018 0.0002994547 0 0.0038813832 0.0034284497 0.0024982518 0.0013227198 0.000307698 0.0039767899 0 0.0052747825 0.0105488189 0.0073894579 2.28346914246428E-020 0.0016659161 0.0002700269 0.0020739384 +C>G CCA C[C>G]A 0.0012849834 2.7772077E-005 0.016832572 0.0105 0.0075375232 0 0.0001 0.0066190772 0.0018 0 0 0.0019 0.0053336514 0 0.0009 0.004 0.0019249788 0.0004584638 0.0002 1.331626E-005 0.0001 0.0005820177 0.0001990492 0.0134768216 0.0072007904 0.0012791061 0.0047306494 0.0001033661 0.0026188632 0 0.0031466824 0.0022969107 0.0094396006 0.001675995 0.0044769459 0.0003355716 0.0008847538 +C>G CCC C[C>G]C 0.0007021348 0.0002796439 0.0135314415 0.0097 0.0076332267 0 0.0004 0.0060777029 0.002 0 0.0002 0.0019 0.0009123035 0 0.0003 0.005 0.0007093678 0.0036542283 0.0028 0.0005481447 0 0.0008252996 0.000283776 0.0161056877 0.0045984731 0.0012149773 0.0012616448 0.0001443108 0.0011115123 0 0.0023630851 0.0028433597 0.0102951282 0.0008310079 0.0027673163 0.000052449 0.0003142141 +C>G CCG C[C>G]G 0.0005062896 1.9161576E-005 0.0041764575 0.0063 0.0026137604 0 0.0006 0.0006560334 0 0 0.0008 0 0.0002854673 0 0.0004 0.0028 3.517869E-006 0.0054057742 0.0002 0 0 0.0003821146 0 0.000797472 0.0008237093 0.0002078326 0.0003608566 0 0.001520047 0.0032461 0.0015435318 0.0054040236 0.0106255283 0.0008310033 0.0018344572 0.000004761 0.0013964056 +C>G CCT C[C>G]T 0.0013815427 0.0003127816 0.0240463904 0.0094 0.0094170979 0.0002 0.0003 0.007805027 0.0039 0 0.0002 0.0019 0.0063830976 0 0.0017 0.008 0.0009537763 0.0055196048 0.0008 0.0001207306 0.0003 0.0017606459 0.0001957753 0.0103886659 0.0001963603 0.0022970262 0.0002680262 0.0002909995 0.0001397507 0 0.00319971 3.70860800590008E-020 0.0068522711 0.0004239346 0.0056157952 0.0001926151 0.0005915023 +C>G GCA G[C>G]A 0.0006021227 4.4838514E-005 0.0119168446 0.007 0.0055594231 0 0 0.0037245679 0.0011 0 0 0.0012 0.0013494196 0.0002 0.0022 0.0031 0.0012963242 0.0009238797 0.002 0.0013397693 0.0004 0 0 0.0049450607 0.0041696555 0.0013206075 0.0014181664 8.1591411E-005 0.0002657599 0.0073775 0.00153378 0.0041577528 0.0048126831 2.28346914246428E-020 0.0030944242 0.0003675084 0.001523035 +C>G GCC G[C>G]C 0.0023933522 1.4520103E-005 0.0098236534 0.0091 0.0053888012 0.003 0.0004 0.003046597 0.0029 0.0002 0.0002 0.0011 0.0007888077 0.0001 0.0005 0.0032 0.0002607609 0.0006486479 0 0.0018111515 0.0042 0 0.0001375011 0.0093698758 0.0023928049 0.0018455011 0.0013467168 0.000105219 0.0009450129 0.0065906 0.0608517207 0.0190915784 0.0509667244 0.0047167891 0.0031230002 1.06168434038267E-020 0.0020402151 +C>G GCG G[C>G]G 2.48534E-007 4.0665889E-005 0.0016710543 0.0062 0.0011005896 0 0 0.0003212128 0 0 0 0 8.1791214E-005 0 0.0006 0 4.377552E-006 0.00054284 0 6.37538E-007 0 0.0002146959 0 0.0056257265 0.0004181939 0.0002050608 0 0 0 0.0015739 3.27595444415171E-020 0.0050892581 0.0129626353 0.0012642272 0.001539434 0.0001210511 0.000894833 +C>G GCT G[C>G]T 0.0008900807 0.0002684295 0.0179143343 0.006 0.0060412478 0.0017 0 0.0057756636 0.0044 0.0004 0 0.0009 0.0026801232 0.0003 0.0018 0.0029 0.0018203928 0.0013767249 0 0.0012382642 0.0004 0.0005384388 0 0.0030557701 0.0019940122 0.0012255329 0.004560686 0.0001596794 0.0047967447 0 0.0086309368 0.022922438 0.011972958 0.0024557172 0.0039954749 0.0005706812 0.000676421 +C>G TCA T[C>G]A 0.0018748532 0.0372418531 0.0160414054 0.0032 0.002681057 0 0.0002 0.0041178788 0.0033 0 0.0001 0.0024 0.2802349465 0 0.0009 0.005 0.0003926847 0.0018029691 0.0005 2.4298469E-005 0.0002 0.0002254906 0.0002306089 0.0102208574 0.0097987246 0.0042018968 0.0028704337 0.0005213704 0.0008204449 0 0.0062124849 0.0015481065 0.0098767034 0.0003657106 0.0027951387 0.0001697674 0.0004808179 +C>G TCC T[C>G]C 0.0020674188 1.9413411E-005 0.0201499204 0.0105 0.0079240483 0.0002 0.001 0.0037996496 0.0025 0 0.0011 0.0027 0.0638852866 0 0.0026 0.0064 0.0006556024 0.0078630068 0.0011 0.0001519986 0.0003 0.000628695 0.000165787 0.0075783653 0.0032665072 0.0028077615 0.0031079676 0.0006673259 0.0004441193 0 0.0046382358 0.0015499829 0.0104195164 2.28346914246428E-020 0.0038186331 0.0009660426 0.0020253166 +C>G TCG T[C>G]G 0.000304897 0.0016254655 0.0025279109 0.0031 0.0013190756 0 0.0003 0.000025653 0 0 0.0003 0 0.009528486 0 0 0 1.3641541E-005 0.0015132233 0 0 0 0.000395808 0 0.0015927142 0.0020574368 6.197E-009 1.2810409E-005 0 0.0001432972 0.0019673 0.0023939233 0.0002293998 0.0040902531 2.28346914246428E-020 0.0026731185 8.65095809094198E-005 0.0006634679 +C>G TCT T[C>G]T 0.0031515745 0.0668798997 0.0326736408 0.005 0.0066445957 0.0001 0.0007 0.0062475537 0.0049 0.0001 0.0008 0.0015 0.3302254817 0.0001 0.0015 0.0169 0.0028523804 0.0035671021 0.0105 0.00068306 0.0003 0.0002573751 0.0004389558 0.0061007272 0.0164009169 0.008019383 0.0021305875 0.0012457795 0.001369869 0 0.0109379855 0.0079398101 0.0198199846 0.0007988588 0.0031000891 0.0004375033 0.00213264 +C>T ACA A[C>T]A 0.0295145327 0.0074415568 0.0178721707 0.012 0.0218391876 0.0312 0 0.0180666872 0.0093 0 0.0225 0.0121 0.0014801808 0.0293 0.0117 0.0135 0.0093504884 0.0038256239 0.0221 0.0328580473 0.0051 0.0031133897 0.0197671544 0.0063155181 0.0209876181 0.005907232 0.0137232858 0.0054337925 0.0051972213 0.065119 0.0012054247 0.0320885261 0.0098060082 0.0225701805 0.0023906012 0.031397907 0.0109990991 +C>T ACC A[C>T]C 0.014322747 0.0027263124 0.0088960343 0.0075 0.0127561056 0.0163 0.0197 0.005650015 0.0056 0.0032 0.1099 0.0054 4.0508707E-005 0.0321 0.0169 0.0076 0.004224289 0.0024652143 0.0203 0.0221960469 0.0062 0.0015248603 0.0818805799 0.0038443269 0.0131412837 0.0106264578 0.005424306 0.0018154155 0.00897647 0.054397 0.0020840175 0.0247589098 0.000014969 0.1193404879 0.0011790037 0.1281792372 1.63618104265282E-020 +C>T ACG A[C>T]G 0.1716469313 0.0033220833 0.0035727084 0.0028 0.0167601771 0.0908 0.0001 0.0192651055 0.0125 0.0126 0.0072 0.0019 0.0003165947 0.0496 0.0309 0.0035 0.0092292133 0.0084639569 0.0368 0.0345720147 0.0256 0.0036256412 0.0092487151 0.0031106644 0.0196598943 0.0199303232 0.0067064295 0.0054320393 0.0316389964 0.0204604 0.0054138542 0.0094650035 0.0135229545 0.0067748274 0.0006406472 0.0049427727 0.0041432056 +C>T ACT A[C>T]T 0.0126237632 0.0033265284 0.0147976122 0.0059 0.0164779547 0.0149 0.0043 0.0208059675 0.0076 0.0047 0.0639 0.0067 0 0.0277 0.0066 0.0101 0.0057359612 0.0056057399 0.0266 0.0188195596 0.003 0 0.0332096522 0.0034204187 0.0057285193 0.0113345306 0.004475614 0.0016292132 0.0047696666 0.0219359 3.27595444415171E-020 0.039006119 0.0014857753 0.071059016 0.001827398 0.105189432 0.0084673356 +C>T CCA C[C>T]A 0.020896447 0.0150195069 0.0143950595 0.021 0.0227692094 0.0085 0.0754 0.00486581 0.0098 0.0012 0.031 0.0187 0.0036472785 0.006 0.0051 0.021 0.0212652059 0.0097675115 0.0438 0.0111451853 0.0034 0.0077313495 0.0605726278 0.0060354474 0.0143339947 0.0065944449 0.0174384848 0.0043915326 0.0091264718 0.0694472 0.0155033821 0.0149734308 0.0134135166 0.0208371809 0.0031630949 0.0221027852 0.0251652379 +C>T CCC C[C>T]C 0.0185017048 0.0035169181 0.0085447812 0.0144 0.0175094763 0.0099 0.1007 0.0039801504 0.0069 0.0024 0.1518 0.0094 0.0010042293 0.0167 0.0088 0.0098 0.0038472353 0.0056548285 0.0753 0.0181527469 0.0091 0.0071108505 0.1863756341 0 0.0059366437 0.006510632 0.0071448702 0.002647661 0.007067603 0.0638403 0.013021492 0.0277530953 0.0035533335 0.1090353647 0.0023361199 0.1200792204 0.0098240362 +C>T CCG C[C>T]G 0.0955772173 0.0049792757 0.0035184658 0.0076 0.0128622376 0.0901 0.0208 0.0083386392 0.0076 0.0109 0.0135 0.0046 0.0001292021 0.0293 0.0155 0.0016 0.0131761123 0.016183223 0.0238 0.0443849425 0.0318 0.005502031 0.0151490826 0.0029244191 0.0115593916 0.0119049353 0.0075035617 0.0022845636 0.0198751804 0.0173126 0.0093878242 0.0106000807 0.0086266994 0.0033373046 0.0008153359 0.0054361338 0.0109032677 +C>T CCT C[C>T]T 0.0171133076 0.0089565528 0.0160755457 0.0201 0.0204295134 0.0087 0.0788 0.0188436274 0.0097 0.0043 0.0816 0.0205 0.00061177 0.0186 0.0096 0.0211 0.0096480253 0.0051533186 0.1159 0.0138471362 0.004 0.0041697772 0.156015397 0.0039712016 0.0136325969 0.0062385563 0.0071480277 0.0024239843 0.0016340587 0.0342318 0.0037452885 0.0170644264 0.0034364665 0.0750337534 0.0023529602 0.0989779779 0.0459700918 +C>T GCA G[C>T]A 0.0249438142 0.0063908079 0.0161272733 0.0087 0.0200382586 0.0653 0 0.0022612627 0.0062 0 0.0261 0.0124 0.0029341376 0.0557 0.0476 0.0125 0.0020687547 0.0027030687 0.0374 0.056793948 0.0163 0.0019153709 0.053282059 0.0236790513 0.010038112 0.009606515 0.0142153137 0.0033842409 0.011638793 0.0485934 0.0048229646 0.0892436272 0.0043067164 0.0306663268 0.0013973066 0.0214764258 0.0106870051 +C>T GCC G[C>T]C 0.027161494 0.0019958168 0.0082086324 0.008 0.0180223122 0.0773 0.021 0.0016166492 0.0069 0.0134 0.0975 0.0092 0.0025151711 0.0618 0.1345 0.0092 0.0003254834 0.0041993075 0.0614 0.0544298573 0.0392 0.0032291335 0.1629183437 0.0159192018 0.0069538752 0.0195074267 0.0201436462 0.001687414 0.0037817517 0.0494787 0.0037100764 0.0856648665 0.0003026637 0.105842878 1.64761887388717E-005 0.0782012229 0.0060785799 +C>T GCG G[C>T]G 0.1035707623 0.000303021 0.0012129229 0.0023 0.0131938176 0.1339 0.0002 0.0116067116 0.0088 0.027 0.009 0.0023 0.0032052646 0.0978 0.1829 0.0009 0.0075111014 0.0118973608 0.0278 0.0045926886 0.0019 0.0033005989 0.0130464947 0.0126480776 0.010468363 0.0225027174 0.0093684685 0.002189309 0.019684388 0.0157387 0.0091644502 0.0308714868 0.0101967765 0.0097694965 0.0014993181 0.0044460527 0.0093497401 +C>T GCT G[C>T]T 0.0176898544 0.0032658182 0.0106116492 0.0082 0.0195029153 0.0524 0.0161 0.006284929 0.0101 0.0152 0.0522 0.0115 0.0016877305 0.0555 0.08 0.0116 0.0009256972 0.0019133809 0.0917 0.0495808638 0.0166 0.0011140596 0.1075903998 0.0181297784 0.0098238207 0.0173074722 0.007589626 0.0010439936 0.0057613368 0.0188865 0.0016456849 0.1762001422 0.000252515 0.0705253792 0.0007327716 0.0704268438 0.0252314948 +C>T TCA T[C>T]A 0.0144920996 0.4199413996 0.0088802091 0.0035 0.0109975603 0.0074 0.1202 0.0071806685 0.005 0.0037 0.0302 0.0138 0.1138420932 0.0092 0.0112 0.0172 0.0161007846 0.0149233917 0.0218 0.0107103221 0.0064 0.0020167217 0.0145586137 0.0265718943 0.0110775208 0.0113032888 0.0187577765 0.0076222577 0.0120765831 0.0849892 0.00612291 0.016765482 0.0101245636 0.0216295113 0.0004213732 0.0198210105 0.0106059003 +C>T TCC T[C>T]C 0.0176807754 0.0819724961 0.0135295728 0.007 0.0206449648 0.0067 0.2887 0.0040610329 0.0084 0.0211 0.1589 0.0095 0.015024839 0.0283 0.0156 0.0131 0.0167799841 0.0099627443 0.033 0.0081755098 0.0086 0.0019908342 0.0435104469 0.0120556911 0.0064487875 0.010807527 0.0079891844 0.0051166192 0 0.090301 0.0108921843 0.0179803954 0.003814104 0.1327623933 0.0020981333 0.1253180687 0.0045197968 +C>T TCG T[C>T]G 0.0760022217 0.0477201864 0.0017054089 0.0011 0.0075344896 0.0391 0.0992 0.0055351215 0.0047 0.2141 0.008 0.001 0.006102098 0.0094 0.0104 0.0036 0.0162720956 0.0115497151 0.009 0.0231638992 0.0126 0.0014984731 0.0027526405 0.0053633597 0.0140834162 0.0103643293 0.004609131 0.0019180281 0.0158301968 0.0151485 0.0014706199 0.0150859914 0.0140381297 0.0050845027 0.000657358 0.0043935397 0.006429352 +C>T TCT T[C>T]T 0.013761704 0.2286749183 0.0103044169 0.0077 0.0117874618 0.0047 0.0844 0.0122090705 0.0096 0.0392 0.0954 0.009 0.0281406612 0.0229 0.0076 0.0193 0.0198274176 0.005398014 0.0267 0.0095400872 0.0064 0.0011822265 0.0243287852 0.0055324992 0.0124185859 0.0072491454 0.0118809325 0.0061931586 0.0134621373 0.045544 0.0038110945 0.0225109222 0.0040578949 0.0981830992 0.0023085876 0.1184227677 0.0281680921 +T>A ATA A[T>A]A 0.0040215203 1.32377E-007 0.0084285636 0.0048 0.0089029043 0.0006 0.001 0.0133650828 0.0121 0 0.0002 0.0058 0.0012436183 0 0.0021 0.0081 0.0006130025 0.0030372108 0.0011 0.0005744014 0.0083 0.0496192297 0 0.0011667471 0.0204305271 0.0044593399 0.143076389 0.0009640309 0 0.0075743 0.0213988628 0.0016153942 0.0036242193 2.28346914246428E-020 0.0044936789 0.0004435178 0.0078378864 +T>A ATC A[T>A]C 0.0023711442 0.0001130696 0.0073730967 0.0039 0.0073992025 0.0033 0.0008 0.0124312021 0.0042 0.0002 0.0001 0.0065 0.0010600019 0.0008 0.009 0.0073 0.0018785875 0.0008111672 0.0053 0.0019714621 0.0292 0.0116667405 0 1.5173057E-005 0.0088925607 0.0128222429 0.0014640854 0.0033656678 0.0030495957 0.003738 0.0046842304 0.0039533946 0.001510433 0.0012607026 0.008807992 0.0004945331 0.0054454405 +T>A ATG A[T>A]G 0.00281091 0.0005329294 0.0073573 0.01 0.0115080515 0 0.0009 0.0140366571 0.0068 0 0.0007 0.0046 0.0001025544 0 0.0009 0.008 0.0010873497 0.0045032071 0.0045 0.0001905866 0.0027 0.0679154542 0.0002374185 0.0063324556 0.0062419485 0.0011723443 0.0012262809 0.0017857537 0.003909982 0.0065906 0.0583714179 0.0049727586 0.0085456931 3.92791895501103E-020 0.0474446131 1.06168434038267E-020 0.0272805461 +T>A ATT A[T>A]T 0.0083609093 0.000149111 0.008753939 0.003 0.0111936232 0.0053 0.0035 0.0241099166 0.0185 0.0012 0.0003 0.006 0.0009718121 0.0009 0.0079 0.0084 0.0020454937 0.0027365232 0.0033 0.0074211035 0.0043 0.0145999176 0 4.967216E-006 0.0148508776 0.0039931375 0.002535198 0.0056530891 0.0051055274 0.0093447 0.0070547539 0.0025332903 0.0049596807 0.0003670923 0.0097010208 0.000250913 0.0076822653 +T>A CTA C[T>A]A 0.0011825874 0.000154599 0.0075713203 0.0075 0.0050431635 0.0001 0 0.0120242175 0.0055 0 0.0004 0.0017 0.000285159 0 0.0016 0.0054 3.0079241E-005 0.0004123464 0.0043 4.5042364E-005 0 0.0868985455 0.0005945285 0.0027666348 0.0262963231 0.0035614227 0.3306010175 0.00256658 0.0017654475 0.0053118 0.0483959361 3.70860800590008E-020 2.80409853263637E-020 0.0004214101 0.0030069836 8.83773649853599E-005 0.016911196 +T>A CTC C[T>A]C 0.0019031669 0.000464019 0.0127254635 0.0111 0.0062088437 0.0026 0.0014 0.0178810924 0.0049 0.0001 0.0011 0.0086 0.0002222873 0.0034 0.0043 0.0128 0.0102237477 0.0024914113 0.0053 0.0043890556 0.0037 0.0537068468 0 0.0026944625 0.0157998831 0.003901611 0.0028135988 0.0196108974 0.0003833591 0.0067873 0.0529238918 0.0055241267 0.0121689451 0.0004418274 0.0464989794 0.0002839599 0.0201908902 +T>A CTG C[T>A]G 0.0014879606 0.0002304098 0.0115085619 0.0342 0.010507569 0.0008 0.0007 0.0163567745 0.0051 0.0003 0.0006 0.0031 0.0002869518 0.0002 0.0027 0.013 0.0044670362 0.0055230457 0.0021 0.0011278358 0.0025 0.2132208666 0.0001731204 0.0069111647 0.0628606064 0.0023903042 0.0043968571 0.0088336 0.0035568452 0.0082628 0.1374715155 0.0042244367 0.0171153481 0.0023322216 0.1759940642 0.0004900921 0.0652277252 +T>A CTT C[T>A]T 0.0021793444 0.0005748856 0.0164561777 0.0115 0.0097846407 0.0011 0.0018 0.0262478019 0.0069 0.0009 0.0004 0.0054 8.00446E-007 0.002 0.0007 0.0096 0.0312448834 0.0033137133 0.0022 0.0023855413 0.001 0.0618275075 0.0004578131 0.0029152002 0.0366223511 0.0016359227 0.0054308916 0.0109426098 0.0022327555 0 0.0421848137 0.0095318815 0.0120375101 0.0032148689 0.0636503124 1.06168434038267E-020 0.0262779434 +T>A GTA G[T>A]A 0.0006892894 0.0001149942 0.0044347826 0.0069 0.0067403877 0 0 0.0081391786 0.003 0 0.0003 0.0015 0.0001379604 0 0 0.003 8.545689E-006 0.0018754341 0.0026 0.0001631298 0 0.0537091457 0 0.0022251273 0.0362178008 0.0022428865 0.109851872 0.0005514608 0.0029300981 0.003738 0.0446039243 3.70860800590008E-020 0.0011458553 2.28346914246428E-020 0.0242716316 0.0003044765 0.0042013058 +T>A GTC G[T>A]C 0.0005524095 0.0002938621 0.0056154324 0.0052 0.0040215965 0.0028 0 0.0079100803 0.0029 0.0001 0.0003 0.0039 0.0002528674 0.0025 0.0038 0.004 0.002573467 0.0015103098 0 0.0037991795 0.0142 0.0094893967 0.0001832038 0.0048531492 0.0058471096 0.0052072871 2.3455678E-005 0.0031639876 0 0.0033445 0.0125235888 0.0030277907 0.0012285467 0.0008083668 0.0179461702 0.0002367232 0.0016197032 +T>A GTG G[T>A]G 0.0012002288 8.8721344E-005 0.0080701365 0.0133 0.0068143523 0.0006 0.0006 0.0090572631 0.0028 0 0.0004 0.0019 0.0001535175 0 0.0026 0.0051 0.0035388226 0.0015053688 0.0016 0.0008283337 0.0031 0.0502939024 0 0.0001957586 0.0382411793 0.0013581218 0.0015659372 0.002152847 0.0005336324 0.0050167 0.0460502984 0.0010906538 0.0077826056 0.0019375384 0.103954526 0.0003980643 0.0218805741 +T>A GTT G[T>A]T 0.0021071368 0.0002157555 0.0086791217 0.0045 0.0051010329 0.0021 0.001 0.0178122386 0.0036 0.0004 0.0001 0.0031 0.0001227456 0.0009 0.0043 0.0033 0.00387901 0.0036110252 0.0052 0.0019007466 0.0041 0.0106014572 0 0 0.0201679544 0.0025131129 0 0.0020077332 0 0.0063939 0.007042014 0.0029648102 0.0046125727 0.0021050728 0.0298636223 0.0002916778 0.0067356063 +T>A TTA T[T>A]A 0.0056001554 8.0752486E-005 0.0071326814 0.0045 0.0092056373 0.0002 0.001 0.0151399962 0.0215 0 0.0003 0.0057 0.0004032613 0 0.0008 0.0085 0.0006988123 0.004663278 0.0039 0.000924548 0.0027 0.0408105028 0 0 0.021830329 0.0006281453 0.0528138875 0.0002032376 0.0011912074 0.0076726 0.0184166439 3.70860800590008E-020 0.002312234 2.28346914246428E-020 0.0040023292 6.85246736359736E-005 0.0119031697 +T>A TTC T[T>A]C 0.0019990793 4.802898E-006 0.0091027978 0.0046 0.0068353442 0.0008 0.0015 0.0120935546 0.0027 0.0008 0 0.0132 0.0007718133 0.0016 0.0019 0.0087 0.0025793586 0.0025781555 0.0048 0.0007082068 0.0045 0.0255703958 0 0.0079941292 0.0034056867 0.0050737539 4.7091785E-005 0.0101809649 0.001682664 0.0064922 0.0160946246 0.0018285335 0.0003268915 0.0012342766 0.0149322709 8.55752603112063E-009 0.0107582495 +T>A TTG T[T>A]G 0.0010900657 0.000066605 0.006565863 0.0082 0.0071442088 0 0.001 0.0083625466 0.014 0 0 0.0037 0.0002451942 0 0.0006 0.0063 2.1133639E-005 0.0020167384 0.0052 9.7003127E-005 0 0.0698452181 0.0002315256 0.0112021436 0.0101915204 2.0138391E-005 0 0.0032504272 0.002438756 0.0036396 0.040365198 0.0032796029 0.0053251107 0.0007275037 0.0496236886 1.06168434038267E-020 0.0207078591 +T>A TTT T[T>A]T 0.0039810228 0.0002763159 0.0147121354 0.0045 0.0102408504 0.0007 0.005 0.0276532963 0.0139 0.0028 0.0008 0.0094 0.000160346 0.0012 0.0003 0.008 0.0038831306 0.0028186794 0.0085 0.0023134891 0.0008 0.0235790618 0 0.0002705788 0.0145275393 0.0012355385 0.0019297708 0.0164928123 0 0 0.0069546395 0.0010941496 0.0014059298 2.28346914246428E-020 0.0123523838 1.06168434038267E-020 0.0111784782 +T>C ATA A[T>C]A 0.013915773 0.0013035096 0.0130357094 0.0084 0.0353667351 0.0075 0.0005 0.0162065101 0.0252 0.0031 0.0006 0.0466 0.0005494542 0.0026 0.0115 0.0717 0.002697314 0.0029330536 0.0145 0.016395063 0.0265 0.0168399309 0.0010684488 0.0047260091 0.0206632828 0.0550286521 0.0050473011 0.0040927469 0.0101191812 0 0.0007369268 0.0018982472 0.0032086778 0.0021449978 0.0012492827 0.0008360974 0.0167611068 +T>C ATC A[T>C]C 0.0062749606 0.0004255767 0.0091862897 0.002 0.0137711021 0.0056 0.0001 0.0077878028 0.0105 0.0052 0.0015 0.0317 0.0001455067 0.0046 0.0073 0.0171 0.0080781501 0.0015132848 0.0048 0.0192517936 0.0165 0.0011082624 0.0002215732 0.0006279493 0.0095024784 0.0275946042 0.0018456912 0.0078807292 0.0063496827 0.0087547 0.0023157171 0.0082384411 0.0047295938 0.0016959289 0.0037492625 0.0014204736 0.0368452578 +T>C ATG A[T>C]G 0.0101376362 0.000575473 0.0117169201 0.0081 0.0284490517 0.0217 0.0007 0.0098525836 0.0176 0.0026 0.0008 0.0487 0.000279178 0.0035 0.0073 0.0348 0.0044328707 0.003329669 0.0135 0.054784918 0.0224 0.0049136164 0.0004988015 0.0027237586 0.0199114925 0.0517910441 0.0056888139 0.0055208336 0.0146596103 0.0090498 0.0117071286 0.0155936441 0.0199843865 0.0033499277 0.0082514297 0.0004135217 0.0267834634 +T>C ATT A[T>C]T 0.0092563164 0.0014881641 0.0169788708 0.0036 0.0273029742 0.0023 0.0011 0.0218294638 0.0247 0.004 0.0003 0.025 0.0002674614 0.0025 0.0063 0.0497 0.0031403702 0.0054913178 0.016 0.0073412699 0.0189 0.0026305239 0.0003132405 0.0071223685 0.0144883903 0.0390722444 0.0025927546 0.003232484 0.0078924134 0 0.0032016902 0.0009747108 0.0057597756 0.0016824476 0.0037991583 1.52941700565386E-005 0.0221085555 +T>C CTA C[T>C]A 0.0041766749 0.0005466192 0.0078950126 0.0052 0.0142386298 0.0062 0.001 0.0051738424 0.0154 0.0005 0.0001 0.0312 4.2751466E-005 0.0006 0.0032 0.0146 0.0074269996 0.0001921693 0.0066 0.0148676965 0.0219 0.0040273463 0 0.0018488765 0.0090280149 0.0378893777 0.0048990792 0.0207380034 0 0 3.27595444415171E-020 3.70860800590008E-020 0.0037334463 0.0012694857 0.0030605132 0.0002793274 0.0094075061 +T>C CTC C[T>C]C 0.0052525933 0.0003923326 0.0144311704 0.0026 0.0124895004 0.004 0.0008 0.0109368938 0.0118 0.0019 0.0004 0.0385 4.3307542E-005 0.0053 0.005 0.0194 0.0396570012 0.0030501926 0.007 0.018356161 0.01 0.0013524439 0 0.0044536899 0.0107716324 0.021740735 0.0057244485 0.0432837972 0.0027749537 0 0.0079452901 3.70860800590008E-020 0.0108649219 0.0037894225 0.0097182676 0.0009258279 0.0446116027 +T>C CTG C[T>C]G 0.0070132253 0.0003620245 0.0084229721 0.01 0.0187416312 0.027 0.001 0.0056577736 0.0154 0.0015 0.0001 0.0415 5.4272534E-005 0.0016 0.0128 0.019 0.0286096963 0.0025964642 0.004 0.0741505626 0.0211 0.0027496661 0.0003207049 0 0.0133506613 0.0472401033 0.005661479 0.0370882617 0.0069024147 0 0.0053848162 0.0065013981 0.0174152084 0.0029716741 0.0100054171 0.0008548023 0.01561524 +T>C CTT C[T>C]T 0.0067138131 0.0005609001 0.0119324305 0.0054 0.0190540829 0.0033 0.0045 0.0111203893 0.0275 0.002 0.0009 0.0324 7.63944E-007 0.0027 0.0035 0.0263 0.1018696577 0.0013100287 0.0053 0.0110011183 0.0204 0.0023633535 0 0.001597389 0.00896103 0.0207406214 0.0039005891 0.005052716 0.0030414249 0 0.0126209242 0.0081108597 0.017359194 0.0016698115 0.0079776445 0.0003108439 0.0303223841 +T>C GTA G[T>C]A 0.0112478351 4.673852E-006 0.0068500556 0.0061 0.0162949828 0.0122 0.0002 0.0057207785 0.0091 0.0064 0.001 0.0573 0.0010540812 0.0078 0.0195 0.0161 1.1401335E-005 0.0005291265 0.0039 0.0024693171 0.1426 0.0042174541 0.0002511686 0.0012697498 0.0174898239 0.0980528247 0.0047773804 0.0036550481 0.0070908038 0 0.0047403321 0.0019137689 0.0019750503 0.0016904982 0.0033999956 0.0020780793 0.0238767847 +T>C GTC G[T>C]C 0.0069997243 0.0001860659 0.006260749 0.0016 0.0095745606 0.0059 0.0001 0.0051810515 0.0097 0.0101 0.0016 0.0274 0.0005298997 0.0127 0.0499 0.0099 0.0096577133 0.0022791308 0.003 0.0015656329 0.0665 0 0.0005382185 0.00671034 0.0040456124 0.040226364 0.0019649543 0.0070711753 0.0071113275 0.0065906 0.0095055012 0.0067394905 0.007108284 0.007601967 0.0066302715 0.0028938432 0.0373426928 +T>C GTG G[T>C]G 0.0049775926 0.000000495 0.006098763 0.0042 0.0141039293 0.0115 0.0003 0.0050407075 0.0094 0.0054 0.0019 0.041 0.0006300957 0.0082 0.0154 0.0148 0.0046541291 0.0058710566 0.006 0.027341755 0.0884 0.0014748845 0 0.000277685 0.0134022463 0.044620701 0.0012291677 0.0082322384 0.0056430636 0.0078694 0.0062721008 0.0110147688 0.0095895668 0.001697214 0.0095595352 0.0017103342 0.0446625918 +T>C GTT G[T>C]T 0.0106674061 0.0005785981 0.0075093439 0.0024 0.0156668747 0.0042 0.0081 0.0084882203 0.0126 0.0124 0.0023 0.0405 0.0006761879 0.0086 0.0094 0.0142 0.0081492346 0.0047715657 0.0099 0.0014982648 0.1003 0.0015610427 0.0009957697 0.0042384777 0.0141596937 0.0555280683 0.003747225 0.0004078845 0.0112376743 0.0084596 0.0022664575 0.0082567832 0.0036822191 0.0016897626 0.0039742914 0.0018309055 0.037512717 +T>C TTA T[T>C]A 0.0080736164 0.0001019324 0.0091154951 0.0028 0.017059641 0.0059 0.0023 0.0049010724 0.0156 0.003 0.0002 0.05 0.0007840561 0.0018 0.0068 0.0246 0.0017085867 0.0003023036 0.0052 0.0057342296 0.0389 0.0048036697 0 0.001682291 0.0145150501 0.0287896805 0.0017210153 0.0099295521 0.011498666 0 0.0014804542 3.70860800590008E-020 0.0005155448 0.0004342265 0.0002008934 2.69491298125691E-005 0.0095996027 +T>C TTC T[T>C]C 0.0048573812 0.0004703437 0.0109537909 0.0016 0.0141957091 0.0035 0.0018 0.0060810113 0.0137 0.0097 0.0009 0.0342 0.0001329749 0.0056 0.0099 0.0183 0.0110741521 0.0062607911 0.002 0.0112342547 0.0313 0.0009121575 0.0002306089 0.0023445277 0.0074060835 0.0366394924 0.0034892126 0.0290105632 0.003584215 0.0091481 0.0007815096 0.001861857 0.0043626179 0.0012602376 0.0045334937 0.0024327604 0.0226722212 +T>C TTG T[T>C]G 0.0083254542 0.0001923542 0.0061130332 0.0036 0.0125965017 0.0106 0.0019 0.0017124847 0.0098 0.0065 0.0007 0.032 3.7402404E-005 0.0034 0.0039 0.0165 0.0059320028 0.0015412653 0.0057 0.0237676113 0.0249 0.0017817357 0.0002395138 0.0004812742 0.0048925312 0.0191436943 0.0011528466 0.0156832186 0.0016942967 0.0060004 0.0007662323 3.70860800590008E-020 0.0026293456 0.0012747632 0.0024208246 0.0006974434 0.0094636702 +T>C TTT T[T>C]T 0.0062571056 0.0005853303 0.0107743363 0.0022 0.0173751391 0.0029 0.0024 0.0100034418 0.0309 0.0099 0.0005 0.0371 0.0001797028 0.0026 0.0047 0.0174 0.0072082184 0.0013577971 0.0038 0.0053951863 0.0274 0 0 0.000358148 0.0170147808 0.0230716888 0.001527957 0.0172915636 0.0037997058 0 0.0032239339 0.0005133397 0.0022567107 2.28346914246428E-020 0.0010789385 0.0009168841 0.0203240337 +T>G ATA A[T>G]A 0.0015876364 3.3718411E-005 0.0023513681 0 0.003462152 0 0 0.0042197193 0.0335 0 0 0.0012 0.0003861998 0 0 0.0052 5.3139249E-005 0.0003861382 0.0014 1.765291E-006 0 0.0016519986 0 0 0.0052816797 8.0653426E-005 0.0011363374 0.0063646756 0 0.0053118 0.0032703303 0.0015043531 0.0028023351 0.0003957761 0.0014441538 9.63385814248833E-005 0.0036558173 +T>G ATC A[T>G]C 0.0017840913 2.4844826E-005 0.0014642311 0.0002 0.0022465927 0.0017 0 0.0007936713 0.0051 0.004 0 0.001 0.0001123832 0.002 0.0006 0.0042 0.0064686613 0.0012549821 0 0.0003813879 0.0031 0 0 0.0014639507 0 0.0001631712 0.0009589764 0.0166109056 0 0.0024592 0.0055761328 3.70860800590008E-020 0.0078161802 0.0016649968 0.0016409129 0.0001054276 0.0009645819 +T>G ATG A[T>G]G 0.0013858306 0.0002734541 0.0090537776 0.0015 0.0054902168 0.0007 0.0009 0.0068658004 0.0052 0.0015 0.0001 0.0018 3.6000696E-005 0.0007 0.0012 0.0061 0.003481549 0.0023692161 0.001 0.0006587581 0.0016 0.0010868728 0 0.0008476125 0.0071364216 0.0012550795 6.766061E-005 0.0065928422 0.0029251714 0.0062955 0.0201754566 0.0174806227 0.0270345909 0.0016119211 0.0052592527 8.9297393290661E-005 0.0025491352 +T>G ATT A[T>G]T 0.0031585393 0.0002176949 0.0070309764 0.0002 0.0038212267 0.0029 0 0.0029399223 0.0193 0.0137 0 0.003 0.0001924938 0.0056 0.0029 0.0076 0.0309263752 0.0003386029 0.0017 0.0005321252 0.0018 0 0 0.0010754553 0 0.0018503835 0.0002560277 0.0863928974 0 0.0095416 0.0054223733 0.0017155767 0.0053889069 0.0008560725 0.0008122481 1.4899146840365E-008 0.0001871482 +T>G CTA C[T>G]A 0.0003026912 0.0001137846 0.0019741811 0 0.0020416489 0.0001 0 0.0024240506 0.0216 0.0022 0 0.0013 1.5094208E-005 0 0 0.0002 9.1469787E-005 6.1002548E-005 0 2.3264084E-005 0 0.0011203565 0 0 0 9.539626E-005 0 0.0095898419 0.0011168548 0.0046233 3.27595444415171E-020 3.70860800590008E-020 0.0005262194 0.0004210208 0.0042847979 0.0002891821 0.001843657 +T>G CTC C[T>G]C 0.0020985024 2.2095087E-005 0.0058242955 0.0013 0.0034785021 0.004 0.0008 0.0020962106 0.0064 0.0018 0.0001 0.0049 0.0001476248 0.002 0.0019 0.0082 0.0198142936 0.0020156969 0.0011 0.0084764945 0.0005 0.0010645836 0.0001901443 0.0021854373 0.0028864543 0.0039194551 0.000381245 0.0339132237 0 0.0060004 0.0039803758 0.0025376549 0.0060513622 2.28346914246428E-020 0.0088482202 0.0009775125 0.0090219017 +T>G CTG C[T>G]G 0.0015995485 0.0002282459 0.0104646545 0.0046 0.0071474562 0.005 0.0009 0.0066040463 0.0126 0.0037 0.0011 0.0045 4.59873E-005 0.0005 0.0007 0.0067 0.0134498376 0.0053119673 0.0013 0.0153837761 0.0004 0.0041885681 0 0.0001139097 0.0117694925 0.0054973573 0.0004032572 0.0185164816 0.0021696933 0.0073775 0.0039200627 0.0028967736 0.007564699 0.0003827374 0.0207298099 1.06168434038267E-020 0.003023422 +T>G CTT C[T>G]T 0.0027585376 6.711134E-005 0.0087243873 0.0012 0.0114868115 0.0086 0.0013 0.0048667139 0.0509 0.0182 0.0009 0.0063 0.0004637147 0.0063 0.0045 0.0186 0.2614566141 0.0023416292 0.0019 0.0021853947 0.0032 0.0016294096 0.000210835 0.0025337183 0.0085508075 0.0067887187 0.0014390961 0.118967103 0.0011436633 0.0091481 0.0157841091 0.012870271 0.0262293556 0.0019670653 0.0047092177 0.0002687511 0.003570495 +T>G GTA G[T>G]A 0.000099045 9.5552392E-005 0.004144488 0 0.0016276645 0 0 0.0009745787 0.0072 0 0 0 1.8489857E-005 0 0 0 3.9193821E-005 0.0013415325 0 3.579149E-006 0 0 0 0 0.0055462269 3.7393232E-005 0 0 0 0.0032461 0.0015356557 0.0019915953 0.0015778632 0.0008546281 0.0021439553 0.0003157141 0.0037470482 +T>G GTC G[T>G]C 0.0002023656 4.7002381E-005 0.0045019853 0 0.0003277349 0.0016 0 0.0005248216 0.0006 0.002 0 0.0004 9.3373513E-005 0.0019 0.0022 0.0032 0.0090784615 9.20431E-007 0 0.0028305751 0.0006 0 0 0.0010736323 0 0.002460705 5.0790565E-005 0 0 0.001869 0.0007606153 0.0041116159 0.0032012845 0.0008454968 0.0013465618 0.0003570074 0.0027277577 +T>G GTG G[T>G]G 0.0011883532 0.0001099257 0.0163914526 0.0018 0.0059488798 0.001 0.0017 0.0060877535 0.005 0.0009 0.001 0.0011 1.0579194E-005 0.0012 0.0037 0.0008 0.0047827755 0.009695 0.0043 0.0027332194 0.0004 0.0018775892 0.0001871324 0.002924697 0.0086852444 0.0008172016 0.0047429186 0.0042178083 0.0036405938 0.0033445 0.0054079152 3.70860800590008E-020 0.002512037 0.0012687784 0.0077472793 0.0015192874 0.0082395121 +T>G GTT G[T>G]T 0.0008007233 8.647718E-005 0.0070672366 0.0002 0.0033074666 0.0035 0.0009 0.0054274338 0.0185 0.003 0 0.0032 5.3741207E-005 0.0038 0.019 0.0044 0.0634977566 0.0028905535 0.0025 0.0035585586 0.0008 0 0 0.0008250983 0.0027685717 0.0078335613 0.002298476 0.0316489973 0.0061810238 0.0056069 0.0101885638 0.0066566288 0.0079578565 0.0029254388 0.0018168896 0.0004726412 0.0032734591 +T>G TTA T[T>G]A 0.0013975537 0.000071737 0.0054271842 0 0.0052028744 0.0009 0 0.0017432214 0.0502 0.005 0 0.0019 0.0005465818 0 0 0.0068 0.0001334106 3.6318404E-005 0.0032 2.69147E-007 0 0.0016516988 0 0 0.0020814799 8.534935E-006 0.0011890225 0.0093896587 0 0.0086563 0.0008187477 0.000948451 0.0005293442 2.28346914246428E-020 0.0002407249 7.25392033429029E-005 0.0017254818 +T>G TTC T[T>G]C 0.001291737 1.4281456E-005 0.0061602504 0.0003 0.0051316079 0.0019 0.001 0.0025498383 0.0081 0.0092 0 0.0027 0.0002353471 0.0015 0.0004 0.0069 0.0096133452 0.003233838 0.0018 0.0003772344 0.0018 0 0 0 0.0005789788 0.0027185098 0.0002802954 0.030117077 0 0.0043282 0.0015336834 0.0010831046 0.0010211012 2.28346914246428E-020 0.0013929045 0.0003332825 0.0037135711 +T>G TTG T[T>G]G 0.0020310769 0.0002066152 0.0110765263 0.003 0.0060552541 0.0011 0.001 0.0060303952 0.0088 0.0022 0.0003 0.0011 0.000000479 0.0002 0.0009 0.0049 0.0045224623 0.0007546018 0.0011 0.0005154216 0.0003 0.002572752 0.0002475019 0.0013605049 0.0094291959 0.0013691612 0.0023530556 0.0126987508 0.000353696 0.0082628 0.0015835907 3.70860800590008E-020 0.003717572 2.28346914246428E-020 0.0039677318 0.0002233266 0.0022664664 +T>G TTT T[T>G]T 0.0040301282 2.3598204E-005 0.0130009842 0.0011 0.0133699358 0.0072 0.0014 0.0072239989 0.0545 0.0633 0.0003 0.0032 0.0006705883 0.0025 0.0033 0.0163 0.0580404078 0.0021264415 0.0013 0.0006156567 0.0003 0 0 6.9515778E-005 0.0078696716 0.0025680767 0.0001395613 0.2336597833 0.0061048341 0 0.0031734006 0.001871395 0.0032018465 2.28346914246428E-020 0.0014171235 0.0003757336 0.0024231362
--- a/R/compareSignature_Galaxy.r Thu Apr 28 03:59:27 2016 -0400 +++ b/R/compareSignature_Galaxy.r Fri Apr 29 05:11:28 2016 -0400 @@ -8,7 +8,7 @@ ######################################################################################################################################### -# Compare new signatures with published one using the cosine similarity method # +# Compare new sigantures with published one using the cosine similarity method # #########################################################################################################################################
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hg18_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,32 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The hg18_listAVDB.txt has this format (white space +#characters are TAB characters): +# +#<RefGenome_DatabaseName> <operation> +# +# +# +#hg18_refGene.txt g +#hg18_genomicSuperDups.txt r +#hg18_snp138.txt f +hg18_refGene.txt g +hg18_knownGene.txt g +hg18_ensGene.txt g +hg18_cytoBand.txt r +hg18_gwasCatalog.txt r +hg18_genomicSuperDups.txt r +hg18_snp138.txt f +hg18_ALL.sites.2014_10.txt f +hg18_AFR.sites.2014_10.txt f +hg18_AMR.sites.2014_10.txt f +hg18_EAS.sites.2014_10.txt f +hg18_EUR.sites.2014_10.txt f +hg18_SAS.sites.2014_10.txt f +hg18_esp6500siv2_all.txt f +hg18_esp6500siv2_aa.txt f +hg18_esp6500siv2_ea.txt f +hg18_ljb26_sift.txt f +hg18_ljb26_pp2hdiv.txt f +hg18_ljb26_pp2hvar.txt f +hg18_cosmic70.txt f +hg18_exac03.txt f
--- a/hg19_listAVDB.txt Thu Apr 28 03:59:27 2016 -0400 +++ b/hg19_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -29,9 +29,11 @@ hg19_ljb26_sift.txt f hg19_ljb26_pp2hdiv.txt f hg19_ljb26_pp2hvar.txt f +hg19_ljb26_mt.txt f hg19_cosmic70.txt f hg19_exac03.txt f hg19_exac03nontcga.txt f hg19_exac03nonpsych.txt f hg19_kaviar20150923.txt f hg19_hrcr1.txt f +hg19_dbscsnv11.txt f
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hg38_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,36 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The hg38_listAVDB.txt has this format (white space +#characters are TAB characters): +# +#<RefGenome_DatabaseName> <operation> +# +# +# +#hg38_refGene.txt g +#hg38_genomicSuperDups.txt r +#hg38_snp142.txt f +hg38_refGene.txt g +hg38_knownGene.txt g +hg38_cytoBand.txt r +hg38_gwasCatalog.txt r +hg38_genomicSuperDups.txt r +hg38_snp142.txt f +hg38_ALL.sites.2015_08.txt f +hg38_AFR.sites.2015_08.txt f +hg38_AMR.sites.2015_08.txt f +hg38_EAS.sites.2015_08.txt f +hg38_EUR.sites.2015_08.txt f +hg38_SAS.sites.2015_08.txt f +hg38_esp6500siv2_all.txt f +hg38_esp6500siv2_aa.txt f +hg38_esp6500siv2_ea.txt f +hg38_ljb26_sift.txt f +hg38_ljb26_pp2hdiv.txt f +hg38_ljb26_pp2hvar.txt f +hg38_cosmic70.txt f +hg38_exac03.txt f +hg38_exac03nontcga.txt f +hg38_exac03nonpsych.txt f +hg38_kaviar20150923.txt f +hg38_hrcr1.txt f +hg38_dbscsnv11.txt f \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mm10_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,17 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The mm10_listAVDB.txt has this format (white space +#characters are TAB characters): +# +#<RefGenome_DatabaseName> <operation> +# +# +# +#mm10_refGene.txt g +#mm10_genomicSuperDups.txt r +#mm10_snp137.txt f +mm10_refGene.txt g +mm10_knownGene.txt g +mm10_ensGene.txt g +mm10_cytoBand.txt r +mm10_genomicSuperDups.txt r +mm10_snp142.txt f
--- a/mutspecAnnot.pl Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecAnnot.pl Fri Apr 29 05:11:28 2016 -0400 @@ -38,7 +38,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -our $max_cpu = 1; # Max number of CPU to use for the annotation +our $max_cpu = 12; # Max number of CPU to use for the annotation # Recover the current path
--- a/mutspecAnnot.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecAnnot.xml Fri Apr 29 05:11:28 2016 -0400 @@ -33,7 +33,6 @@ <data name="output" type="data" format="tabular" label="${input.name} annotated" /> </outputs> - <stdio> <regex match="ANNOVAR LOG FILE" source="stdout" @@ -118,7 +117,9 @@ **ANNOVAR annotations** -An example of annotations retrieved by the tool. +An example of annotations retrieved by the tool (for the full list please visit the Galaxy pages `Annovar databases`__) + +.. __: http://galaxy.iarc.fr/galaxy/u/ardinm/p/annovar-databases Gene-based: RefSeqGene, UCSC Known Gene and Ensembl Gene @@ -169,13 +170,25 @@ </help> + <citations> <citation type="bibtex"> - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } </citation> </citations>
--- a/mutspecCompare.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecCompare.xml Fri Apr 29 05:11:28 2016 -0400 @@ -109,11 +109,22 @@ <citations> <citation type="bibtex"> - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } </citation> </citations>
--- a/mutspecFilter.pl Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecFilter.pl Fri Apr 29 05:11:28 2016 -0400 @@ -45,7 +45,7 @@ # Zero databases is specified if( ($dbSNP == 0) && ($segDup == 0) && ($esp == 0) && ($thG == 0) ) { - print STDERR "There is no databases selected for filtering against!!!\nPlease choose at least one between dbSNP, SegDup, ESP (only for human genome) or 1000 genome (only for human genome)\n"; + print STDERR "There is no databases selected for filtering against!!!\nPlease chose at least one between dbSNP, SegDup, ESP (only for human genome) or 1000 genome (only for human genome)\n"; exit; }
--- a/mutspecFilter.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecFilter.xml Fri Apr 29 05:11:28 2016 -0400 @@ -97,11 +97,22 @@ <citations> <citation type="bibtex"> - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } </citation> </citations>
--- a/mutspecNmf.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecNmf.xml Fri Apr 29 05:11:28 2016 -0400 @@ -108,11 +108,22 @@ <citations> <citation type="bibtex"> - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } </citation> </citations>
--- a/mutspecNmf_wrapper.sh Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecNmf_wrapper.sh Fri Apr 29 05:11:28 2016 -0400 @@ -3,7 +3,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -cpu=1 +cpu=8 @@ -13,7 +13,7 @@ source=$1;shift input=$1 -if [[ $source == "html" ]] +if [[ $source == "html" ]] then input=${input%%.*}_files/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt fi @@ -44,7 +44,7 @@ else echo "<td> <center> <a href="NMF/Figures/Heatmap_MixtureCoeff.png">" >> $html echo "<img src="NMF/Figures/Heatmap_MixtureCoeff.png" /></a> <center> </td>" >> $html -fi +fi echo "</tr>" >> $html echo "</table>" >> $html
--- a/mutspecSplit.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecSplit.xml Fri Apr 29 05:11:28 2016 -0400 @@ -85,11 +85,22 @@ <citations> <citation type="bibtex"> - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } </citation> </citations>
--- a/mutspecStat.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecStat.xml Fri Apr 29 05:11:28 2016 -0400 @@ -156,11 +156,22 @@ <citations> <citation type="bibtex"> - @ARTICLE{ardin_mutspec:_2016, - author = {Ardin et al}, - keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}, + @article{ardin_mutspec:_2016, title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes}, - url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z} + volume = {17}, + issn = {1471-2105}, + doi = {10.1186/s12859-016-1011-z}, + shorttitle = {{MutSpec}}, + abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}. + {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool. + {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.}, + pages = {170}, + number = {1}, + journaltitle = {{BMC} Bioinformatics}, + author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali}, + date = {2016}, + pmid = {27091472}, + keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions} } </citation> </citations>
--- a/mutspecStat_wrapper.sh Thu Apr 28 03:59:27 2016 -0400 +++ b/mutspecStat_wrapper.sh Fri Apr 29 05:11:28 2016 -0400 @@ -3,7 +3,7 @@ ######################################### ### SPECIFY THE NUMBER OF CPU ### ######################################### -cpu=1 +cpu=8 @@ -119,9 +119,9 @@ touch $outEstimateSign echo "<a href='Mutational_Analysis/EstimatingSignatures.html'>Estimating the number of signatures</a><br/>" >> $html echo "<br/> <center> <h2>Computed statistics for estimating the number of signatures</h2> </center> <br/>" >> $outEstimateSign - echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/> + echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/> Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing, <br/> - Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/> + Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/> Frigyesi et al. 2008, considered the smallest value at which the decrease in the RSS is lower than the decrease of the RSS obtained from random data. <br/><br/> The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate. <br/> <br/> The original data are shuffled for comparing the quality measures obtained with our data (Data x) and from randomized data (Data y). The curves for the actual data are in solid line, those for the randomized data are in dashed line. <br/> <br/>" >> $outEstimateSign
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rn6_listAVDB.txt Fri Apr 29 05:11:28 2016 -0400 @@ -0,0 +1,14 @@ +#This is a sample file distributed with Galaxy that is used by the +#MutSpec-Annot tools. The hg18_listAVDB.txt has this format (white space +#characters are TAB characters): +# +#<RefGenome_DatabaseName> <operation> +# +# +# +#rn6_refGene.txt g +#rn6_genomicSuperDups.txt r +#rn6_snp138.txt f +rn6_refGene.txt g +rn6_ensGene.txt g +rn6_snp146.txt f \ No newline at end of file
--- a/tool_dependencies.xml Thu Apr 28 03:59:27 2016 -0400 +++ b/tool_dependencies.xml Fri Apr 29 05:11:28 2016 -0400 @@ -3,8 +3,8 @@ <set_environment version="1.0"> <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> - - <package name="perl" version="5.18.1"> + + <package name="perl" version="5.18.1"> <install version="1.0"> <actions> <action type="setup_perl_environment"> @@ -43,7 +43,7 @@ <repository changeset_revision="57b37f63cb84" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="R" version="3.1.2"> + <package name="R" version="3.1.2"> <repository changeset_revision="4d2fd1413b56" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package>